FDA Unveils Its Approach to Infectious Disease Sequencing DiagnosticsFDA Unveils Its Approach to Infectious Disease Sequencing Diagnostics

FDA has published a draft guidance document explaining its perspective on diagnostics devices that use next-generation sequencing to identify infectious diseases. In the draft guidance, "Infectious Disease Next Generation Sequencing Based Diagnostic Devices: Microbial Identification and Detection of Antimicrobial Resistance and Virulence Markers," the agency describes its "systems approach" to regulating these diagnostic devices and proposes the use of the FDA-ARGOS database as an alternative comparator.

The technology is a crucial one and accuracy is key. Next-generation sequencing diagnostics for infectious disease "carry an absolute need for immediate and actionable results, sometimes within hours, as an incorrect initial diagnosis potentially leads to fatalities," FDA noted. 

The draft guidance developed out of discussions on the topic from an April 2014 FDA public workshop and an April 2015 colloquium held by the American Society for Microbiology. 

Next-generation sequencing can be used to identify one or several different organisms and combines the functions of what were previously many tests into one process, FDA explained. Yet there is a wide range of infectious diseases and many types of samples tested with each device, including spit, urine, blood, stool, cerebrospinal fluid. FDA suggests the "one system" approach similar to its method of oversight for other molecular-based diagnostics. "This approach will evaluate, in parallel, the system as a whole (including generation of clinically actionable data), and each individual step in the sequencing data pipeline as part of that system, from specimen collection to results report," according to the draft guidance document.

Indeed, the draft guidance includes a figure showing the steps in the sequencing process that are covered by FDA oversight: specimen collection, specimen preparation for sequencing, sequencing/chemistry/data collection, data storage/data analysis, and the report. If creating the final report also includes databases, or genome assembly, annotation, and finishing, these steps may also be part of FDA's purview.

The agency has also proposed that sponsors use the FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS); BioProject 231221 as an alternative comparator for clinical evaluation of pathogens, antimicrobia resistance, and virulence markers, part of a "least burdensome regulatory approach," the document stated.

According to the FDA document, sponsors should include information on the device description and validation in a submission. Intended use, test methodology, ancillary reagents, controls, and details on interpreting tests results and reports should be included in the device description, while pre-analytical factors, device performance metrics, analytical performance, instrumentation and software, and clinical evaluation should be part of the device validation section.

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